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- PDB-5brk: pMob1-Lats1 complex -

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Basic information

Entry
Database: PDB / ID: 5brk
TitlepMob1-Lats1 complex
Components
  • MOB kinase activator 1A
  • Serine/threonine-protein kinase LATS1
KeywordsTransferase/Signaling protein / pMob1 / Lats1 / Hippo / Transferase-Signaling protein complex
Function / homology
Function and homology information


inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / regulation of ubiquitin-dependent protein catabolic process / regulation of transforming growth factor beta receptor signaling pathway / sister chromatid segregation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of actin filament polymerization / hippo signaling / regulation of postsynaptic density assembly / mammary gland epithelial cell differentiation ...inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / regulation of ubiquitin-dependent protein catabolic process / regulation of transforming growth factor beta receptor signaling pathway / sister chromatid segregation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of actin filament polymerization / hippo signaling / regulation of postsynaptic density assembly / mammary gland epithelial cell differentiation / regulation of intracellular estrogen receptor signaling pathway / regulation of organ growth / Signaling by Hippo / negative regulation of protein localization to nucleus / positive regulation of NLRP3 inflammasome complex assembly / microtubule organizing center / protein kinase activator activity / regulation of protein-containing complex assembly / keratinocyte differentiation / hormone-mediated signaling pathway / protein serine/threonine kinase activator activity / nuclear estrogen receptor binding / negative regulation of canonical Wnt signaling pathway / G1/S transition of mitotic cell cycle / spindle pole / G2/M transition of mitotic cell cycle / intracellular protein localization / midbody / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / postsynapse / protein phosphorylation / positive regulation of apoptotic process / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / glutamatergic synapse / magnesium ion binding / extracellular exosome / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase LATS1, catalytic domain / : / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / UBA/TS-N domain / Protein kinase, C-terminal ...Serine/threonine-protein kinase LATS1, catalytic domain / : / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / UBA/TS-N domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase LATS1 / MOB kinase activator 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsNi, L. / Luo, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM085004 United States
CitationJournal: Genes Dev. / Year: 2015
Title: Structural basis for Mob1-dependent activation of the core Mst-Lats kinase cascade in Hippo signaling.
Authors: Ni, L. / Zheng, Y. / Hara, M. / Pan, D. / Luo, X.
History
DepositionMay 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOB kinase activator 1A
B: Serine/threonine-protein kinase LATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1173
Polymers39,0522
Non-polymers651
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-15 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.833, 73.338, 53.910
Angle α, β, γ (deg.)90.00, 99.06, 90.00
Int Tables number5
Space group name H-MC121
DetailsDimer by Gel Filtration

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Components

#1: Protein MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B


Mass: 25563.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / Plasmid: pGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) T1 / References: UniProt: Q9H8S9
#2: Protein Serine/threonine-protein kinase LATS1 / Large tumor suppressor homolog 1 / WARTS protein kinase / h-warts


Mass: 13488.567 Da / Num. of mol.: 1 / Fragment: UNP residues 602-704
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LATS1, WARTS / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) T1
References: UniProt: O95835, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density meas: 0.172 Mg/m3 / Density % sol: 49.08 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M di-Ammonium citrate 20% (W/V) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15456 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.134 / Rsym value: 0.126 / Net I/σ(I): 16.51
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 0.428 / % possible all: 80.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.057 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 2564 10.04 %Random selection
Rwork0.1857 ---
obs0.1892 13818 80.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 1 64 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042182
X-RAY DIFFRACTIONf_angle_d0.7982938
X-RAY DIFFRACTIONf_dihedral_angle_d16.367828
X-RAY DIFFRACTIONf_chiral_restr0.03311
X-RAY DIFFRACTIONf_plane_restr0.003376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33530.2594710.2163589X-RAY DIFFRACTION37
2.3353-2.3830.3234880.2201811X-RAY DIFFRACTION52
2.383-2.43480.25391030.2162935X-RAY DIFFRACTION58
2.4348-2.49140.21411070.2264940X-RAY DIFFRACTION61
2.4914-2.55370.28661120.2111044X-RAY DIFFRACTION66
2.5537-2.62270.29641250.21931072X-RAY DIFFRACTION70
2.6227-2.69990.30461350.22581209X-RAY DIFFRACTION75
2.6999-2.7870.27571350.23231227X-RAY DIFFRACTION79
2.787-2.88660.2591390.20581305X-RAY DIFFRACTION83
2.8866-3.00220.24011620.20641450X-RAY DIFFRACTION90
3.0022-3.13870.27661700.21021491X-RAY DIFFRACTION94
3.1387-3.30420.21171660.20941516X-RAY DIFFRACTION97
3.3042-3.51110.2331720.17971544X-RAY DIFFRACTION98
3.5111-3.7820.19691720.16991564X-RAY DIFFRACTION99
3.782-4.16230.21131750.15711580X-RAY DIFFRACTION100
4.1623-4.76380.17031750.14751555X-RAY DIFFRACTION100
4.7638-5.99890.17981790.16241588X-RAY DIFFRACTION100
5.9989-41.0640.20271780.18781559X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1356-0.8789-0.0872.68472.8917.6628-0.361-0.12090.0081-0.7766-0.11710.40760.6119-0.11880.13360.66910.01590.03370.2845-0.0120.347127.136928.7763-9.8575
22.0161-0.4034-1.23484.99960.68724.4941-0.02490.2098-0.154-0.2905-0.205-0.05440.49650.04480.08060.23330.0020.00660.2605-0.01510.193128.46932.38486.7412
32.9983-0.3806-1.10964.87020.21184.37630.2218-0.14330.012-0.22-0.3225-0.6410.13720.05360.01970.13680.00710.01490.26310.04190.19229.631936.65157.6498
42.3526-0.3565-0.91194.56090.39672.6101-0.14980.5056-0.1429-0.82360.00220.97720.2828-0.8730.01660.4067-0.1183-0.09950.3413-0.06550.237518.583233.94822.6491
51.8921-2.6624-1.99363.79383.56993.8321-0.1329-0.0086-0.31360.0482-0.14720.84030.1376-0.30650.26160.2363-0.03820.04130.23330.00240.28513.624741.740223.5887
69.1322-6.3491-3.14724.97023.38484.41370.3945-0.04810.3513-0.3584-0.0353-0.0822-0.6012-0.1266-0.26010.4179-0.07890.07030.2261-0.04490.171319.968156.697424.5581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 172 )
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 212 )
5X-RAY DIFFRACTION5chain 'B' and (resid 635 through 671 )
6X-RAY DIFFRACTION6chain 'B' and (resid 672 through 698 )

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